plotTracks
.Several additional display parameters (i.e. displayPars(foo)=list(...)
are defined for this class, including
plot.anchors
which can be used to specify whether anchors are to be drawn. col.anchors.line
which can be used
to alter the colour of border of these anchor elements and col.anchors.fill
can be used to alter the fill colour of these
elements. The value of plot.outside
determines whether or not interactions
which span outside of the window are to be plotted, and col.outside
defines the colour of these interactions.
Similarly plot.trans
determines whether trans-interactions are plotted and col.trans
specifies the colour
of trans-interactions. By default, the height of an arc representing an interaction is proportional to the number
of reads/counts supporting that interaction. Instead of using the counts to define this, the height can be set to
be proportional to either fdr
or p.value
using the interaction.measure
display parameter. By changing the
interaction.dimension
to width, the line widths of each arc now represent the statistic supporting them. The heights of the arcs
can be made to be proportional to log10 of the supporting statistic by changing interaction.dimension.transform
to log. col.interactions
sets the colour of arcs representing interactions within the region of interest. It is possible to colour the arcs by the type
of interaction they are involved in (i.e. promoter-promoter interactions etc) by setting the col.interactions.types
display parameter to be a named vector of colours, where the name corresponds to the type of interaction. This is applicable to
anchors regions through the use of the col.anchors.line.node.class
and col.anchors.fill.node.class
parameters.